def test_good_file(self, request_mock):
with full_rig_with_s3() as (app, engine):
upload_id = self.do_upload(app, request_mock)
# okay, here's what we really want to test.
# call the merge endpoint
response = app.post(
'/api/upload/merge_file?uploadId={}'.format(upload_id))
response_data = json.loads(response.get_data().decode('utf-8'))
assert response_data['status'] == 'success'
# make sure that there is a new merged file on s3
expected_s3_path = 's3://test-bucket/boone/hmis_service_stays/merged'
with open_sesame(expected_s3_path, 'rb') as expected_s3_file:
reader = csv.reader(expected_s3_file)
assert len([row for row in reader]) == ROWS_IN_GOOD_HMIS_FILE
# and make sure that the merge log has a record of this
assert db_session.query(MergeLog).filter(
MergeLog.upload_id == '123-456').one
# make sure that the master table has been bootstrapped
master_table = generate_master_table_name('boone',
'hmis_service_stays')
total_rows = db_session.query(
'count(*) from {}'.format(master_table)).one()
assert total_rows == (ROWS_IN_GOOD_HMIS_FILE - 1, )
# make sure that we filled in some matched ids
total_rows = db_session.query(
'count(matched_id is not null) from {}'.format(
master_table)).one()
assert total_rows == (ROWS_IN_GOOD_HMIS_FILE - 1, )
def test_write_matches_to_db(self):
BOOTSTRAPPED_HMIS_FILE = 'sample_data/matched/bootstrapped_hmis_data_20180401.csv'
MATCHES_HMIS_FILE = 'sample_data/matched/matchesonly_hmis_data.csv'
with testing.postgresql.Postgresql() as postgresql:
db_engine = create_engine(postgresql.url())
create_and_populate_master_table(table_name='hmis_service_stays',
db_engine=db_engine,
file_path=BOOTSTRAPPED_HMIS_FILE)
# generate expected matches by taking the first column of the matched id spreadsheet
with open(MATCHES_HMIS_FILE, 'rb') as f:
reader = csv.reader(f, delimiter='|')
next(reader)
expected_matched_ids = set(
re.sub(r'\W+', '', row[0]) for row in reader)
# write these matches to the DB
with open(MATCHES_HMIS_FILE, 'rb') as fh:
write_matches_to_db(db_engine=db_engine,
event_type='hmis_service_stays',
jurisdiction='boone',
matches_filehandle=fh)
full_table_name = generate_master_table_name(
'boone', 'hmis_service_stays')
retrieved_matched_ids = set([
row[0] for row in db_engine.execute(
'select distinct matched_id from {}'.format(
full_table_name))
])
assert retrieved_matched_ids == expected_matched_ids
def test_update_overlapping(self):
with testing.postgresql.Postgresql() as postgresql:
engine = create_engine(postgresql.url())
Base.metadata.create_all(engine)
db_session = scoped_session(
sessionmaker(autocommit=False, autoflush=False, bind=engine))
self.populate_seed_data(db_session)
# merge in a table with one new row and one row that has the same
# primary key but a new name: hopefully we won't be seeing much like
# this in production but we do want to be sure that we use the new
# data in these cases (for instance, data corrections)
OLD = '456780'
UPDATED = '456789'
NEW = '456791'
raw_table_name = '234-567'
new_data = [
[
u'123458', UPDATED, 'A345', 'Jack F. Ripper', '1896-04-10',
'345-45-6789'
],
[
u'123459', NEW, 'A345', 'Jack R. Ripper', '1896-04-10',
'345-45-6780'
],
]
create_and_populate_raw_table('234-567', new_data, db_session.bind)
upsert_raw_table_to_master(raw_table_name, self.jurisdiction,
self.event_type, '234-567', db_session)
master_table_name = generate_master_table_name(
self.jurisdiction, self.event_type)
result = self.get_pks_and_names(master_table_name, db_session)
assert len(result) == 4
# the duplicated event id should only be present once
assert result == [
('456780', 'A345', 'Jack L. Ripper'),
('456780', 'A346', 'Jack L. Ripper'),
('456789', 'A345', 'Jack F. Ripper'),
('456791', 'A345', 'Jack R. Ripper'),
]
# let's check the timestamps
timestamp_result = dict(
(row[0], (row[1], row[2])) for row in db_session.execute('''
select "internal_event_id", "inserted_ts", "updated_ts" from {}
'''.format(master_table_name)))
# created timestamp of an old row that was not updated should be the same as an old row that was updated
assert timestamp_result[OLD][0] == timestamp_result[UPDATED][0]
# updated timestamp of an old row that was not updated should be lower than an old row that was updated
assert timestamp_result[OLD][1] < timestamp_result[UPDATED][1]
# created and updated timestamps of totally new rows should be equivalent
assert timestamp_result[NEW][0] == timestamp_result[NEW][1]
merge_logs = db_session.query(MergeLog).all()
assert len(merge_logs) == 2
assert merge_logs[0].upload_id == '123-456'
assert merge_logs[1].upload_id == '234-567'
assert merge_logs[0].total_unique_rows == 3
assert merge_logs[1].total_unique_rows == 2
assert merge_logs[0].new_unique_rows == 3
assert merge_logs[1].new_unique_rows == 1
def sync_merged_file_to_storage(jurisdiction, event_type, db_engine):
full_path = merged_file_path(jurisdiction, event_type)
table_name = generate_master_table_name(jurisdiction, event_type)
with open_sesame(full_path, 'wb') as outfile:
cursor = db_engine.raw_connection().cursor()
copy_stmt = 'copy "{}" to stdout with csv header delimiter as \'|\''.format(
table_name)
cursor.copy_expert(copy_stmt, outfile)
def source_data_to_filehandle(jurisdiction, event_type):
master_table = generate_master_table_name(jurisdiction, event_type)
out_filehandle = io.BytesIO()
cursor = db.engine.raw_connection().cursor()
copy_stmt = 'copy {} to stdout with csv header delimiter as \',\''.format(
master_table)
cursor.copy_expert(copy_stmt, out_filehandle)
out_filehandle.seek(0)
return out_filehandle
def create_merged_table(jurisdiction, event_type, db_session):
master_table_name = generate_master_table_name(jurisdiction, event_type)
goodtables_schema = load_schema_file(event_type)
full_column_list = master_table_column_list(goodtables_schema)
create = create_statement_from_column_list(full_column_list,
master_table_name,
goodtables_schema['primaryKey'])
# create table if it does not exist
logging.info('Assembled create-if-not-exists table statement: %s', create)
db_session.execute(create)
def create_and_populate_merged_table(table_name, data, db_engine):
schema = load_schema_file('test')
n_fields = len(schema['fields'])
for row in data:
assert len(row) == n_fields, "sample merged data must have same # of fields as test schema"
placeholder_string = ', '.join(['%s'] * n_fields)
master_table_name = generate_master_table_name('test', 'test')
column_list = master_table_column_list(schema)
create = create_statement_from_column_list(column_list)
db_engine.execute(create)
for row in data:
db_engine.execute('insert into "{}" values ({}, now(), now())'.format(master_table_name, placeholder_string), *row)
def upsert_raw_table_to_master(raw_table_name, jurisdiction, event_type,
upload_id, db_session):
create_merged_table(jurisdiction, event_type, db_session)
master_table_name = generate_master_table_name(jurisdiction, event_type)
goodtables_schema = load_schema_file(event_type)
base_column_list = column_list_from_goodtables_schema(goodtables_schema)
# use new postgres 'on conflict' functionality to upsert
update_statements = [
' "{column}" = EXCLUDED."{column}"'.format(column=column_def[0])
for column_def in base_column_list
]
start_ts = datetime.today()
insert_sql = '''
insert into {master}
select raw.*, '{new_ts}' inserted_ts, '{new_ts}' updated_ts, row_number() over ()::text || '{event_type}' as matched_id
from "{raw}" as raw
on conflict ({primary_key})
do update set {update_string}, updated_ts = '{new_ts}'
'''.format(raw=raw_table_name,
master=master_table_name,
event_type=event_type,
primary_key=', '.join([
"\"{}\"".format(col)
for col in goodtables_schema['primaryKey']
]),
update_string=', '.join(update_statements),
new_ts=start_ts.isoformat())
logging.info('Executing insert: %s', insert_sql)
db_session.execute(insert_sql)
end_ts = datetime.today()
merge_log = MergeLog(
upload_id=upload_id,
total_unique_rows=total_unique_rows(raw_table_name,
goodtables_schema['primaryKey'],
db_session),
new_unique_rows=new_unique_rows(master_table_name, start_ts,
db_session),
merge_start_timestamp=start_ts,
merge_complete_timestamp=end_ts,
)
db_session.add(merge_log)
db_session.execute('drop table "{}"'.format(raw_table_name))
db_session.commit()
return merge_log.id
def create_and_populate_master_table(table_name, db_engine, file_path=None):
full_table_name = generate_master_table_name('boone', table_name)
create_table_query = f"""
DROP TABLE IF EXISTS {full_table_name};
CREATE TABLE {full_table_name} ({DATA_FIELDS[table_name]})"""
db_engine.execute(create_table_query)
if file_path:
df = pd.read_csv(file_path)
df['internal_event_id'] = df['internal_event_id'].apply(str)
df['matched_id'] = df['matched_id'].apply(str)
if table_name == "jail_bookings":
df['booking_number'] = df['booking_number'].apply(lambda x: str(x) if x else None)
df['jail_entry_date'] = pd.to_datetime(df['jail_entry_date'])
df['jail_exit_date'] = pd.to_datetime(df['jail_exit_date'])
df.to_sql(full_table_name, db_engine, if_exists='append', index=False)
db_engine.execute("update {} set booking_number = null where booking_number = 'nan'".format(full_table_name))
elif table_name == "hmis_service_stays":
df['client_location_start_date'] = pd.to_datetime(df['client_location_start_date'])
df['client_location_end_date'] = pd.to_datetime(df['client_location_end_date'])
df.to_sql(full_table_name, db_engine, if_exists='append', index=False)
def test_update_nonoverlapping(self):
with testing.postgresql.Postgresql() as postgresql:
engine = create_engine(postgresql.url())
Base.metadata.create_all(engine)
db_session = scoped_session(
sessionmaker(autocommit=False, autoflush=False, bind=engine))
# do initial insert, representing the first time data is uploaded
self.populate_seed_data(db_session)
raw_table_name = '234-567'
new_data = [
[
u'123458', u'456790', 'A345', 'Jack F. Ripper',
'1896-04-10', '345-45-6789'
],
[
u'123459', u'456791', 'A345', 'Jack R. Ripper',
'1896-04-10', '345-45-6780'
],
]
create_and_populate_raw_table('234-567', new_data, db_session.bind)
upsert_raw_table_to_master(raw_table_name, self.jurisdiction,
self.event_type, '234-567', db_session)
master_table_name = generate_master_table_name(
self.jurisdiction, self.event_type)
result = self.get_pks_and_names(master_table_name, db_session)
assert len(result) == 5
assert result == [
('456780', 'A345', 'Jack L. Ripper'),
('456780', 'A346', 'Jack L. Ripper'),
('456789', 'A345', 'Jack T. Ripper'),
('456790', 'A345', 'Jack F. Ripper'),
('456791', 'A345', 'Jack R. Ripper'),
]
merge_logs = db_session.query(MergeLog).all()
assert len(merge_logs) == 2
assert merge_logs[0].upload_id == '123-456'
assert merge_logs[1].upload_id == '234-567'
assert merge_logs[0].total_unique_rows == 3
assert merge_logs[1].total_unique_rows == 2
assert merge_logs[0].new_unique_rows == 3
assert merge_logs[1].new_unique_rows == 2
def expunge(jurisdiction, event_type):
"""Expunges all data for a given jurisdiction and event type"""
base_path = app_config['base_path'].format(jurisdiction=jurisdiction, event_type=event_type)
match_cache_path = app_config['match_cache_path'].format(jurisdiction=jurisdiction)
master_table = generate_master_table_name(jurisdiction, event_type)
msg = 'Expunge all data for jurisdiction {} and event_type {}?'.format(jurisdiction, event_type)
msg += '\n\nstorage paths (recursive!): {}, {}'.format(base_path, match_cache_path)
msg += '\n\ndatabase tables: {}'.format(master_table)
msg += '\n\nYou should not do this while the system is validating or matching.'
msg += '\n\nRemove all this?'
shall = input("%s (y/N) " % msg).lower() == 'y'
click.echo(shall)
if not shall:
click.echo("Expunge aborted")
click.echo("Truncating master database table " + master_table)
engine.execute('truncate {}'.format(master_table))
click.echo("Removing base path " + base_path)
remove_recursively(base_path)
click.echo("Removing match cache path" + match_cache_path)
remove_recursively(match_cache_path)
def test_new_table(self):
with testing.postgresql.Postgresql() as postgresql:
engine = create_engine(postgresql.url())
Base.metadata.create_all(engine)
db_session = scoped_session(
sessionmaker(autocommit=False, autoflush=False, bind=engine))
# do initial insert, representing the first time data is uploaded
self.populate_seed_data(db_session)
master_table_name = generate_master_table_name(
self.jurisdiction, self.event_type)
result = self.get_pks_and_names(master_table_name, db_session)
assert len(result) == 3
assert result == [
('456780', 'A345', 'Jack L. Ripper'),
('456780', 'A346', 'Jack L. Ripper'),
('456789', 'A345', 'Jack T. Ripper'),
]
merge_logs = db_session.query(MergeLog).all()
assert len(merge_logs) == 1
assert merge_logs[0].upload_id == '123-456'
assert merge_logs[0].total_unique_rows == 3
assert merge_logs[0].new_unique_rows == 3
def get_records_by_time(start_time, end_time, jurisdiction, limit, offset,
order_column, order, set_status):
hmis_table = generate_master_table_name(jurisdiction, 'hmis_service_stays')
bookings_table = generate_master_table_name(jurisdiction, 'jail_bookings')
hmis_exists = table_exists(hmis_table, db.engine)
bookings_exists = table_exists(bookings_table, db.engine)
if not hmis_exists:
raise ValueError(
'HMIS table {} does not exist. Please try again later.'.format(
hmis_table))
if not bookings_exists:
raise ValueError(
'Bookings table {} does not exist. Please try again later.'.format(
bookings_table))
columns = [
("matched_id::text", 'matched_id'),
("coalesce(hmis_summary.first_name, jail_summary.first_name)",
'first_name'),
("coalesce(hmis_summary.last_name, jail_summary.last_name)",
'last_name'),
("hmis_summary.hmis_id", 'hmis_id'),
("hmis_summary.hmis_contact", 'hmis_contact'),
("hmis_summary.last_hmis_contact", 'last_hmis_contact'),
("hmis_summary.cumu_hmis_days", 'cumu_hmis_days'),
("jail_summary.jail_id", 'jail_id'),
("jail_summary.jail_contact", 'jail_contact'),
("jail_summary.last_jail_contact", 'last_jail_contact'),
("jail_summary.cumu_jail_days", 'cumu_jail_days'),
("jail_summary.percent_bookings_homeless_flag",
"percent_bookings_homeless_flag"),
("coalesce(hmis_summary.hmis_contact, 0) + coalesce(jail_summary.jail_contact, 0)",
'total_contact'),
]
if not any(alias == order_column for expression, alias in columns):
raise ValueError(
'Given order column expression does not match any alias in query. Exiting to avoid SQL injection attacks'
)
base_query = """WITH booking_duration_lookup AS (
select coalesce(nullif(booking_number, ''), internal_event_id) as booking_id,
max(coalesce(location_date::text, jail_entry_date)) as most_recent_location_date,
max(case when jail_exit_date is not null
then date_part('day', jail_exit_date::timestamp - jail_entry_date::timestamp)::int \
else date_part('day', updated_ts::timestamp - jail_entry_date::timestamp)::int
end) as length_of_stay,
bool_or(coalesce(homeless, 'N') = 'Y') as any_homeless
FROM (
SELECT
*
FROM {booking_table}
WHERE
not (jail_entry_date < %(start_date)s AND jail_exit_date < %(start_date)s) and
not (jail_entry_date > %(end_date)s AND jail_exit_date > %(end_date)s)
) AS jail
group by 1
), hmis_summary AS (
SELECT
matched_id::text,
string_agg(distinct internal_person_id::text, ';') as hmis_id,
sum(
case when client_location_end_date is not null
then date_part('day', client_location_end_date::timestamp - client_location_start_date::timestamp) \
else date_part('day', updated_ts::timestamp - client_location_start_date::timestamp)
end
)::int as cumu_hmis_days,
count(*) AS hmis_contact,
to_char(max(client_location_start_date::timestamp), 'YYYY-MM-DD') as last_hmis_contact,
max(first_name) as first_name,
max(last_name) as last_name
FROM (
SELECT
*
FROM {hmis_table}
WHERE
not (client_location_start_date < %(start_date)s AND client_location_end_date < %(start_date)s) and
not (client_location_start_date > %(end_date)s AND client_location_end_date > %(end_date)s)
) AS hmis
GROUP BY matched_id
), jail_summary AS (
SELECT
matched_id::text,
string_agg(distinct coalesce(nullif(internal_person_id, ''), inmate_number)::text, ';') as jail_id,
sum(jail.length_of_stay) as cumu_jail_days,
count(distinct(coalesce(nullif(booking_number, ''), internal_event_id))) AS jail_contact,
to_char(max(jail_entry_date::timestamp), 'YYYY-MM-DD') as last_jail_contact,
max(first_name) as first_name,
max(last_name) as last_name,
round(100 * count(case when any_homeless then 1 else null end) / count(*)::float)::text || '%%' as percent_bookings_homeless_flag
FROM (
SELECT
*
FROM {booking_table}
join booking_duration_lookup bdl on (
bdl.booking_id = coalesce(nullif(booking_number, ''), internal_event_id)
and bdl.most_recent_location_date = coalesce(location_date::text, jail_entry_date)
)
WHERE
not (jail_entry_date < %(start_date)s AND jail_exit_date < %(start_date)s) and
not (jail_entry_date > %(end_date)s AND jail_exit_date > %(end_date)s)
) AS jail
GROUP BY matched_id
)
SELECT
{columns}
FROM hmis_summary
FULL OUTER JOIN jail_summary USING(matched_id)
""".format(
hmis_table=hmis_table,
booking_table=bookings_table,
columns=",\n".join("{} as {}".format(expression, alias)
for expression, alias in columns),
)
logging.info('Querying table records')
if order not in {'asc', 'desc'}:
raise ValueError(
'Given order direction is not valid. Exiting to avoid SQL injection attacks'
)
if not isinstance(limit, int) and not limit.isdigit() and limit != 'ALL':
raise ValueError(
'Given limit is not valid. Existing to avoid SQL injection attacks'
)
filter_by_status = {
'Jail': 'jail_summary.matched_id is not null',
'HMIS': 'hmis_summary.matched_id is not null',
'Intersection': 'hmis_summary.matched_id = jail_summary.matched_id'
}
status_filter = filter_by_status.get(set_status, 'true')
rows_to_show = [
dict(row) for row in db.engine.execute(
"""
{}
where {}
order by {} {} nulls last
limit {} offset %(offset)s""".format(base_query, status_filter,
order_column, order, limit),
start_date=start_time,
end_date=end_time,
offset=offset,
)
]
query = """
SELECT
*,
DATE_PART('day', {exit}::timestamp - {start}::timestamp) as days
FROM {table_name}
WHERE
not ({start} < %(start_time)s AND {exit} < %(start_time)s) and
not ({start} > %(end_time)s AND {exit} > %(end_time)s)
"""
hmis_query = query.format(table_name=hmis_table,
start="client_location_start_date",
exit="client_location_end_date")
bookings_query = query.format(table_name=bookings_table,
start="jail_entry_date",
exit="jail_exit_date")
logging.info('Done querying table records')
logging.info('Querying venn diagram stats')
venn_diagram_stats = next(
db.engine.execute('''select
count(distinct(hmis.matched_id)) as hmis_size,
count(distinct(bookings.matched_id)) as bookings_size,
count(distinct(case when hmis.matched_id = bookings.matched_id then hmis.matched_id else null end)) as shared_size,
count(distinct(matched_id))
from ({}) hmis
full outer join ({}) bookings using (matched_id)
'''.format(hmis_query, bookings_query),
start_time=start_time,
end_time=end_time))
counts_by_status = {
'HMIS': venn_diagram_stats[0],
'Jail': venn_diagram_stats[1],
'Intersection': venn_diagram_stats[2]
}
logging.info('Done querying venn diagram stats')
venn_diagram_data = [{
"sets": ["Jail"],
"size": venn_diagram_stats[1]
}, {
"sets": ["Homeless"],
"size": venn_diagram_stats[0]
}, {
"sets": ["Jail", "Homeless"],
"size": venn_diagram_stats[2]
}]
logging.info('Retrieving bar data from database')
filtered_data = retrieve_bar_data(hmis_table, bookings_table, start_time,
end_time)
logging.info('Done retrieving bar data from database')
filtered_data['tableData'] = rows_to_show
return {
"vennDiagramData": venn_diagram_data,
"totalTableRows": counts_by_status.get(set_status,
venn_diagram_stats[3]),
"filteredData": filtered_data
}
def write_matches_to_db(db_engine, event_type, jurisdiction,
matches_filehandle):
goodtables_schema = load_schema_file(event_type)
table_name = generate_master_table_name(event_type=event_type,
jurisdiction=jurisdiction)
logging.info('Writing matches for %s / %s to table %s', event_type,
jurisdiction, table_name)
reader = csv.reader(matches_filehandle, delimiter='|')
ordered_column_names = next(reader)
matches_filehandle.seek(0)
# 1. create pseudo-temporary table for the raw matches file
# use the CSV's column order but grab the definitions from the goodtables schema
unordered_column_list = column_list_from_goodtables_schema(
goodtables_schema)
primary_key = goodtables_schema['primaryKey']
all_columns = [
('matched_id', 'varchar')
] + [col for col in unordered_column_list if col[0] in primary_key]
column_definitions = dict((col[0], col) for col in all_columns)
ordered_column_list = [
column_definitions[ordered_column_name]
for ordered_column_name in ordered_column_names
]
logging.info('Final column list for temporary matches-only table: %s',
ordered_column_list)
create = create_statement_from_column_list(ordered_column_list, table_name,
primary_key)
temp_table_name = 'temp_matched_merge_tbl'
create = create.replace(table_name, temp_table_name)
logging.info(create)
db_engine.execute(create)
# 2. copy data from filehandle to
conn = db_engine.raw_connection()
cursor = conn.cursor()
pk = ','.join([col for col in primary_key])
copy_stmt = 'copy {} from stdin with csv header delimiter as \'|\' force not null {}'.format(
temp_table_name, pk)
try:
logging.info(copy_stmt)
cursor.copy_expert(copy_stmt, matches_filehandle)
logging.info('Status message after COPY: %s', cursor.statusmessage)
for notice in conn.notices:
logging.info('Notice from database connection: %s', notice)
conn.commit()
cursor = conn.cursor()
cursor.execute('select * from {} limit 5'.format(temp_table_name))
logging.info('First five rows: %s', [row for row in cursor])
big_query = """
update {matched_table} as m set matched_id = regexp_replace(tmp.matched_id::text, '[^\w]', '', 'g')
from {temp_table_name} tmp where ({pk}) """.format(
create=create,
matched_table=table_name,
temp_table_name=temp_table_name,
pk=' and '.join([
'tmp.{col} = m.{col}'.format(col=col) for col in primary_key
]))
logging.info('Updating matches in %s with rows from %s', table_name,
temp_table_name)
logging.info(big_query)
cursor.execute(big_query)
logging.info('Status message after UPDATE: %s', cursor.statusmessage)
conn.commit()
except Exception as e:
logging.error(
'Error encountered! Rolling back merge of matched ids. Original error: %s',
str(e))
conn.rollback()
finally:
db_engine.execute('drop table if exists {}'.format(temp_table_name))